DNA cruciform arms nucleate through a correlated but asynchronous cooperative mechanism.

@article{Matek2012DNACA,
  title={DNA cruciform arms nucleate through a correlated but asynchronous cooperative mechanism.},
  author={Christian Matek and Thomas E. Ouldridge and A Levy and Jonathan P. K. Doye and Ard A. Louis},
  journal={The journal of physical chemistry. B},
  year={2012},
  volume={116 38},
  pages={
          11616-25
        }
}
Inverted repeat (IR) sequences in DNA can form noncanonical cruciform structures to relieve torsional stress. We use Monte Carlo simulations of a recently developed coarse-grained model of DNA to demonstrate that the nucleation of a cruciform can proceed through a cooperative mechanism. First, a twist-induced denaturation bubble must diffuse so that its midpoint is near the center of symmetry of the IR sequence. Second, bubble fluctuations must be large enough to allow one of the arms to form a… 
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